Particle-based liquid array technologies offer a variety of advantages over fixed arrays, such as batch methods of moiety attachment, ease of synthesis, less cost in implementation, ease of automation, and ease of augmentation (i.e., another particle can be added to the mixture). Fixed arrays generally require less expensive reading devices than liquid arrays and they are generally more amenable to archival storage. However, the major advantage of fixed arrays, and the reason they hold a dominant position in applications requiring high multiplexing (e.g., gene expression), is that moiety identity is determined by position, thereby allowing a virtually limitless number of assays to be carried out using a fixed array platform—typical fixed arrays used in gene expression display 100s of thousands of different moieties. In contrast, liquid arrays require that each particle be encoded in order to identify the moiety each particle is displaying.
A variety of methods have been employed to solve the encoding/decoding problem of liquid arrays. One widely used approach (used by Luminex, Invitrogen via Quantum Dots, and BD Biosciences) is to incorporate fluorophors into beads. The fluorophors are mixed in differing ratios to produce the coding structure and variation. The emitted wavelengths and intensities of these fluorophor mixes are read using a technology based on Fluorescence Activated Cell Sorters (FACS). Although effective, this technology is limited by the number of dyes and intensities that can be unambiguously encoded. The limit for this method is currently between 100 to 200 codes.
BioArray Solutions has used Light-controlled Electrokinetic Assembly of Particles near Surfaces (LEAPS) to form arrays of beads on surfaces (WO 97/40385). However, the LEAPS approach is still subject to the same restrictions as bead-based techniques with respect to the types of available encoding.
A system incorporating the advantages of planar arrays and of encoded microparticles would address many of the problems inherent in the existing approaches. Illumina, Inc. has made it halfway to this goal by providing a method of generating arrays of microbeads using etched glass fibers (e.g., “High-density fiber-optic DNA random microsphere array” by Ferguson et al. Anal. Chem., 72:5618-5624 (2000)). The method involves binding a capture molecule (e.g., oligonucleotide) to a microparticle in solution and then permanently attaching the microparticle to a solid support that interfaces directly with etched glass fibers. The identity of the capture molecule on the microparticle can be identified by “visualization” of the particle through the fiber-optic cable on which it is bound. This binding, however, is not reversed and the particle remains as part of a planar array when the assay is performed—its identity being associated with its fixed location. While preparation of the array is facilitated by the liquid or 3D method, the actual assay is performed as if the array were a fixed 2D array.
Cyvera (now part of Illumina) has developed a technology that uses microparticles shaped like cans that are uniquely identified using a Bragg grating (U.S. Patent Application 2005/0220408 A1). This technique does not rely on fluorescence dye encoding and therefore has an inherently greater breadth of encoding space. Other companies have developed microparticles that do not depend on encoding using fluorophors. Nanoplex uses long and skinny photolithographically-prepared particles that are identified by differing fluorescence and reflection of bar-coded patterns composed of metals. They currently have the capacity to uniquely label 1000 of these particles and have proprietary software that identifies the location of, and decodes these particles in about one second after they have settled in a non-ordered fashion to the bottom of 96 well plate or similar. SmartBeads Technologies has microfabricated aluminum particles (e.g., strip particles having dimensions of 100×10×1 micron) encoded using multiple hole placement and decoded using an optical reading device (e.g. CCD) after being scattered on a planar surface at low density. While, in general, these and similar microfabricated particles have the advantage that they have the potential to be encoded with a nearly infinite number of patterns, the difficulty resides in the ease of analysis of mixtures of the encoded particles. Since such particles tend to be flat objects, they tend to be more prone to aggregation or overlapping as well as being more difficult to disperse.
The ability to array microparticles in an ordered fashion for analysis is advantageous. Aviva Biosciences and the research group of Eiichi Tamiya have produced and arrayed optically encoded planar particles. The Tamiya group produces and uses chemical properties to array particles ((“Microfabrication of encoded microparticle array for multiplexed DNA hybridization detection” by Zhi et al. Chemical Communications, 2448-2450 (2005)). Aviva Biosciences uses the magnetic properties of their microparticles (i.e., magnetic bars encapsulated in silicon dioxide with a 2D barcode for identification) to form linear arrays or “chains” of partially overlapping microparticles in the presence of a magnetic field allowing their codes to be read (U.S. Pat. No. 7,015,047). It is also possible to form linear arrays of these magnetic particles in specially designed channels in a non-overlapping manner (U.S. Pat. No. 7,015,047). Another method of arraying Aviva's microparticles to avoid obstruction of the 2D barcode involves incorporating an excess of “accessory” or blank particles (consisting only of completely transparent SiO2 with magnetic bars) into the microparticle mix. This reduces the likelihood of the encoding portion of the microparticles overlapping and increases readability (U.S. Pat. No. 7,015,047).
Although methods for arraying beads using arraying chips that consist of either arrays of magnetic bars or electromagnetic pads have been developed, these approaches suffer from similar limitations of encoding and detection as experienced by other liquid array bead-based methods.
This application references various patents, patent applications, and publications. The contents of all of these items are hereby incorporated by reference in their entirety. Where a definition or use of a term in a reference, which is incorporated by reference herein is inconsistent or contrary to the definition of that term provided herein, the definition of that term provided herein applies and the definition of that term in the reference does not apply.